3fbm

From Proteopedia

(Difference between revisions)

Revision as of 06:31, 25 December 2014

D431N Mutant VP2 Protein of Infectious Bursal Disease Virus; Derived T=1 Particles

Structural highlights

3fbm is a 1 chain structure with sequence from Infectious bursal disease virus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	2gsy
Gene:	CAPSID PROTEIN VP2 (Infectious bursal disease virus)
Resources:	FirstGlance, OCA, RCSB, PDBsum

Function

[POLS_IBDVB] Capsid protein VP2 self assembles to form an icosahedral capsid with a T=13 symmetry, about 70 nm in diameter, and consisting of 260 VP2 trimers. The capsid encapsulates the genomic dsRNA. VP2 is also involved in attachment and entry into the host cell by interacting with host ITGA4/ITGB1.^[1] The precursor of VP2 plays an important role in capsid assembly. First, pre-VP2 and VP2 oligomers assemble to form a procapsid. Then, the pre-VP2 intermediates may be processed into VP2 proteins by proteolytic cleavage mediated by VP4 to obtain the mature virion. The final capsid is composed of pentamers and hexamers but VP2 has a natural tendency to assemble into all-pentameric structures. Therefore pre-VP2 may be required to allow formation of the hexameric structures (By similarity).^[2] Protease VP4 is a serine protease that cleaves the polyprotein into its final products. Pre-VP2 is first partially cleaved, and may be completely processed by VP4 upon capsid maturation (By similarity).^[3] Capsid protein VP3 plays a key role in virion assembly by providing a scaffold for the capsid made of VP2. May self-assemble to form a T=4-like icosahedral inner-capsid composed of at least 180 trimers. Plays a role in genomic RNA packaging by recruiting VP1 into the capsid and interacting with the dsRNA genome segments to form a ribonucleoprotein complex. Additionally, the interaction of the VP3 C-terminal tail with VP1 removes the inherent structural blockade of the polymerase active site. Thus, VP3 can also function as a transcriptional activator (By similarity).^[4] Structural peptide 1 is a small peptide derived from pre-VP2 C-terminus. It destabilizes and perforates cell membranes, suggesting a role during entry (By similarity).^[5] Structural peptide 2 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity).^[6] Structural peptide 3 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity).^[7] Structural peptide 4 is a small peptide derived from pVP2 C-terminus. It is essential for the virus viability (By similarity).^[8]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Viral capsids are envisioned as vehicles to deliver the viral genome to the host cell. They are nonetheless dynamic protective shells since they participate in numerous processes of the virus cycle such as assembly, genome packaging, binding to receptors and uncoating among others. In so doing, they undergo large-scale conformational changes. Capsid proteins with essential enzymatic activities are being described more frequently. Here we show that the precursor (pVP2) of the capsid protein VP2 of the infectious bursal disease virus (IBDV), an avian dsRNA virus, has autoproteolytic activity. The pVP2 C-terminal region is first processed by the viral protease VP4. VP2 Asp431, lying in a flexible loop preceding the C-terminal most a-helix, is responsible for the endopeptidase activity that cleaves the Ala441-Phe442 bond to generate the mature VP2 polypeptide. The Asp431Asn substitution abrogates the endopeptidase activity without introducing a significant conformational change, as deduced from the three-dimensional structure of the mutant protein at 3.1 A resolution. Combinations of VP2 polypeptides containing mutations affecting either the cleavage or the catalytic site revealed that pVP2 proteolytic processing is the result of a monomolecular cis-cleavage reaction. The D431N mutation does not affect the assembly of the VP2 trimers that constitute the capsid building block. Althougth VP2 D431N trimers are capable of assembling both pentamers and hexamers, expression of a polyprotein gene harboring the D431N mutation does not result in the assembly of IBDV virus-like particles. Reverse genetics analyses demonstrate that pVP2 self-processing is essential for the assembly of an infectious IBDV progeny.

Autoproteolytic activity derived from the infectious bursal disease virus capsid protein.,Irigoyen N, Garriga D, Navarro A, Verdaguer N, Rodriguez JF, Caston JR J Biol Chem. 2009 Jan 14. PMID:19144647^[9]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Caston JR, Martinez-Torrecuadrada JL, Maraver A, Lombardo E, Rodriguez JF, Casal JI, Carrascosa JL. C terminus of infectious bursal disease virus major capsid protein VP2 is involved in definition of the T number for capsid assembly. J Virol. 2001 Nov;75(22):10815-28. PMID:11602723 doi:http://dx.doi.org/10.1128/JVI.75.22.10815-10828.2001
↑ Caston JR, Martinez-Torrecuadrada JL, Maraver A, Lombardo E, Rodriguez JF, Casal JI, Carrascosa JL. C terminus of infectious bursal disease virus major capsid protein VP2 is involved in definition of the T number for capsid assembly. J Virol. 2001 Nov;75(22):10815-28. PMID:11602723 doi:http://dx.doi.org/10.1128/JVI.75.22.10815-10828.2001
↑ Caston JR, Martinez-Torrecuadrada JL, Maraver A, Lombardo E, Rodriguez JF, Casal JI, Carrascosa JL. C terminus of infectious bursal disease virus major capsid protein VP2 is involved in definition of the T number for capsid assembly. J Virol. 2001 Nov;75(22):10815-28. PMID:11602723 doi:http://dx.doi.org/10.1128/JVI.75.22.10815-10828.2001
↑ Caston JR, Martinez-Torrecuadrada JL, Maraver A, Lombardo E, Rodriguez JF, Casal JI, Carrascosa JL. C terminus of infectious bursal disease virus major capsid protein VP2 is involved in definition of the T number for capsid assembly. J Virol. 2001 Nov;75(22):10815-28. PMID:11602723 doi:http://dx.doi.org/10.1128/JVI.75.22.10815-10828.2001
↑ Caston JR, Martinez-Torrecuadrada JL, Maraver A, Lombardo E, Rodriguez JF, Casal JI, Carrascosa JL. C terminus of infectious bursal disease virus major capsid protein VP2 is involved in definition of the T number for capsid assembly. J Virol. 2001 Nov;75(22):10815-28. PMID:11602723 doi:http://dx.doi.org/10.1128/JVI.75.22.10815-10828.2001
↑ Caston JR, Martinez-Torrecuadrada JL, Maraver A, Lombardo E, Rodriguez JF, Casal JI, Carrascosa JL. C terminus of infectious bursal disease virus major capsid protein VP2 is involved in definition of the T number for capsid assembly. J Virol. 2001 Nov;75(22):10815-28. PMID:11602723 doi:http://dx.doi.org/10.1128/JVI.75.22.10815-10828.2001
↑ Caston JR, Martinez-Torrecuadrada JL, Maraver A, Lombardo E, Rodriguez JF, Casal JI, Carrascosa JL. C terminus of infectious bursal disease virus major capsid protein VP2 is involved in definition of the T number for capsid assembly. J Virol. 2001 Nov;75(22):10815-28. PMID:11602723 doi:http://dx.doi.org/10.1128/JVI.75.22.10815-10828.2001
↑ Caston JR, Martinez-Torrecuadrada JL, Maraver A, Lombardo E, Rodriguez JF, Casal JI, Carrascosa JL. C terminus of infectious bursal disease virus major capsid protein VP2 is involved in definition of the T number for capsid assembly. J Virol. 2001 Nov;75(22):10815-28. PMID:11602723 doi:http://dx.doi.org/10.1128/JVI.75.22.10815-10828.2001
↑ Irigoyen N, Garriga D, Navarro A, Verdaguer N, Rodriguez JF, Caston JR. Autoproteolytic activity derived from the infectious bursal disease virus capsid protein. J Biol Chem. 2009 Jan 14. PMID:19144647 doi:M808942200

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3fbm"

@@ Line 3: / Line 3: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[3fbm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Infectious_bursal_disease_virus Infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FBM FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2gsy|2gsy]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2gsy|2gsy]]</td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CAPSID PROTEIN VP2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10995 Infectious bursal disease virus])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CAPSID PROTEIN VP2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10995 Infectious bursal disease virus])</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3fbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fbm RCSB], [http://www.ebi.ac.uk/pdbsum/3fbm PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3fbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fbm RCSB], [http://www.ebi.ac.uk/pdbsum/3fbm PDBsum]</span></td></tr>
-<table>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/POLS_IBDVB POLS_IBDVB]] Capsid protein VP2 self assembles to form an icosahedral capsid with a T=13 symmetry, about 70 nm in diameter, and consisting of 260 VP2 trimers. The capsid encapsulates the genomic dsRNA. VP2 is also involved in attachment and entry into the host cell by interacting with host ITGA4/ITGB1.<ref>PMID:11602723</ref>   The precursor of VP2 plays an important role in capsid assembly. First, pre-VP2 and VP2 oligomers assemble to form a procapsid. Then, the pre-VP2 intermediates may be processed into VP2 proteins by proteolytic cleavage mediated by VP4 to obtain the mature virion. The final capsid is composed of pentamers and hexamers but VP2 has a natural tendency to assemble into all-pentameric structures. Therefore pre-VP2 may be required to allow formation of the hexameric structures (By similarity).<ref>PMID:11602723</ref>   Protease VP4 is a serine protease that cleaves the polyprotein into its final products. Pre-VP2 is first partially cleaved, and may be completely processed by VP4 upon capsid maturation (By similarity).<ref>PMID:11602723</ref>   Capsid protein VP3 plays a key role in virion assembly by providing a scaffold for the capsid made of VP2. May self-assemble to form a T=4-like icosahedral inner-capsid composed of at least 180 trimers. Plays a role in genomic RNA packaging by recruiting VP1 into the capsid and interacting with the dsRNA genome segments to form a ribonucleoprotein complex. Additionally, the interaction of the VP3 C-terminal tail with VP1 removes the inherent structural blockade of the polymerase active site. Thus, VP3 can also function as a transcriptional activator (By similarity).<ref>PMID:11602723</ref>   Structural peptide 1 is a small peptide derived from pre-VP2 C-terminus. It destabilizes and perforates cell membranes, suggesting a role during entry (By similarity).<ref>PMID:11602723</ref>   Structural peptide 2 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity).<ref>PMID:11602723</ref>   Structural peptide 3 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity).<ref>PMID:11602723</ref>   Structural peptide 4 is a small peptide derived from pVP2 C-terminus. It is essential for the virus viability (By similarity).<ref>PMID:11602723</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 36: @@
 </StructureSection>
 [[Category: Infectious bursal disease virus]]
-[[Category: Caston, J R.]]
+[[Category: Caston, J R]]
-[[Category: Garriga, D.]]
+[[Category: Garriga, D]]
-[[Category: Irigoyen, N.]]
+[[Category: Irigoyen, N]]
-[[Category: Navarro, A.]]
+[[Category: Navarro, A]]
-[[Category: Rodriguez, J F.]]
+[[Category: Rodriguez, J F]]
-[[Category: Verdaguer, N.]]
+[[Category: Verdaguer, N]]
 [[Category: Autoproteolytic activity]]
 [[Category: Capsid maturation]]

3fbm

From Proteopedia

Revision as of 06:31, 25 December 2014

D431N Mutant VP2 Protein of Infectious Bursal Disease Virus; Derived T=1 Particles

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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